It is generally believed that supragingival plaque control has little effect on the subgingival microflora of deep periodontal pockets. However, this may not be true for moderately deep pockets (4-5 mm), which may represent a pathological state between gingivitis and marginal periodontitis. In 6 patients with poor oral hygiene and severe gingival inflammation, 4 matched sites (1 in each quadrant), were chosen which demonstrated at least 20% spirochetes and 15% black-pigmented Gram-negative bacilli. During the first 12 weeks (phase 1), supragingival calculus was removed from the right half of the mouth and then the teeth were professionally cleaned three times a week. At the beginning of phase 2, supragingival calculus was also removed from the left quadrants and the entire mouth was subjected to the same protocol used in phase 1. At no time did patients receive oral hygiene instructions. Clinical parameters were assessed and microbiological samples were taken at 3-week intervals. Samples were submitted to darkfield microscopy and anaerobic culturing. Analysis by multiple linear regression and the Wilcoxon signed-rank test revealed significant changes in the composition of the subgingival microbiota at cleaned sites. While Gram-positive organisms increased proportionally, a number of putative periodontal pathogens, such as P. gingivalis and spirochetes decreased.